After an incident at work that involved deleting an entire project I discovered a dangerous bug (or feature) in base R functions file.copy() and file.create().

Let’s first create a directory and a file inside it.

dir.create("foo")
cat(file = "foo/bar", "baz\n")
readLines("foo/bar")
#> [1] "baz"

We’ll then permanently delete the file contents.

file.copy("foo", ".", recursive = TRUE)
#> [1] TRUE
readLines("foo/bar")
#> character(0)

What happens?

Looking at file.copy() code, we can see that from and to are checked in an if statement if (recursive && to %in% from), but because "foo" is not ".", the statement is not triggered. If it had been, the function would have stopped stop("attempt to copy a directory to itself").

It looks like (there’s a call to C code) file.copy() then goes on to read the files in from and file.create() them in to directory. file.create() has another interesting property: it doesn’t check if the file already exists. It goes on to create the file, which already exists, and removes all its contents.

A fix

Obviously, from needs to be checked if it’s the same as to and in the current if statement this is attempted. However it only checks if these two strings are exactly the same, but copying a directory to its own parent directory doesn’t trigger the condition. We need to check if to is in the parent directory of from.

if (recursive && (to %in% from || 
      normalizePath(dirname(normalizePath(from))) == normalizePath(to)))

Here normalizePath() is used because it, according to its help file, “Convert[s] file paths to canonical form for the platform, to display them in a user-understandable form and so that relative and absolute paths can be compared.” dirname() outputs different path form so both input and output of dirname() need to be put through normalizePath().

Another option would be to see if from %in% list.files(to) but I think this could be slow if to is a large directory.

If we use the if statement with normalizePath() in an otherwise identical function called file.copy2(), we can’t copy the directory to itself.

file.copy2("foo", ".", recursive = TRUE)
#> Error in file.copy2("foo", ".", recursive = TRUE): attempt to copy a directory to itself